I can't say goodbye again
by Vala-sg1
Summary: A year after her they lost her to the Replicators, Elizabeth suddenly reappears on the Alpha Site. John/Elizabeth, mentions of Rodney/Katie Brown


"I knew I would find you here."

Elizabeth Weir was startled at the interruption. "Janus."

"I hadn't seen you in a while, I thought I would come find you before the others noticed your absence. You know they don't like you being here." The hovering figure nodded down at the blue planet she'd been watching.

"I know they don't. It's just-" she produced a sigh, or the ascended version of one, since she didn't have any lungs, nor she needed air to breathe. "I can't stay away. I never move too close, but I need to know they're still there."

"Elizabeth," he pleaded, then shook his head. Or what she perceived as head. Their explanation for the phenomenon hadn't clarified much for her, but she stopped trying to make sense of it long ago. "You're just as stubborn as I remember you."  
She laughed, and then they were both silent as they watched two puddle jumpers leave the central tower and zip into space past them towards the Midway Station. Elizabeth wondered who was on board the jumpers, and what their mission was.

"We have to go." Janus stated.

"Yes." The resignation in her voice must have been palpable, because then Janus said the unthinkable.

"Would you like to go back?" He asked, surprising her.

She shook her head. "You know I would, but the others-"

"The others know I'm a bit of a rebel. It's not the first time I disobey my superiors for you."

"Janus-"

"You can do so much more down there than twiddling your incorporeal thumbs for eternity wishing you could be somewhere else."

"Janus, this is dangerous, you can't-"

"Shh." He shushed her. His human figure faded into a puddle of light and she felt absolute warmth and calm as he melded with her. The blissful sensation lasted only a brief moment, and then everything was black.

***

"So, Weir pulled a Jackson, uh?"

Sam's smile at Jack's quip was small and tense, but she welcomed the lightness of his tone after the strained briefing she had with Woolsey and IOA officials over Dr. Elizabeth Weir's unexpected return.

"We don't know yet. For all we know it could be an elaborate ruse by the Asurans. Who knows what they might have gotten out of Weir in the months she was with them." Sam licked her lips nervously, bringing up on her tablet the report of her recovery in the Alpha Site. She had read it over and over since Lorne had handed it in. "Keller is running every test that she can. McKay is there as well."

"Daniel coming tomorrow?"

"Yes. I'm gating back to Atlantis in the morning to greet the IOA delegation. It will be nice to see a familiar face among all these bureaucrats. And it will be good for Elizabeth to have someone to relate to."

"Assuming she's the real deal and not a clone planted by the Asurans to destroy the city, that is."

"That is." Sam echoed, sighing tiredly. The radio she had temporarily discarded on her desk started beeping incessantly.

"This must be Keller. I'm afraid I have to go now, Jack. I'll talk to you as soon as possible."  
"Of course," he said, a hint of disappointment in his voice, "keep me posted, Carter, will ya?"

"Will do. Carter out." Sam ran a hand through her hair and readjusted her earpiece, tapping on the earphone to allow communication. "Carter here."

Keller's voice greeted her "Colonel, this is Dr. Keller."  
"Doctor, is this about Dr. Weir?" Sam could hear Rodney talking animatedly in background as she strode to the infirmary building. "is she okay?"  
_Are we safe?_ Every time the question popped into her mind she felt guilty. Elizabeth had been missing for the better part of a year, presumed dead at the hands of the Asurans, and while a part of her hoped that it was the real Elizabeth Weir that had been found, naked and confused, in the woods outside the Athosian settlement, her guard was high. If the Asurans had somehow discovered the location of their Alpha site...

"Yes, we have been running tests and I think you might want to see the results for yourself." Keller did not sound alarmed, which somewhat reassured Sam that Elizabeth was not in danger nor posed an immediate threat to them or the city. However, the hesitation in her voice gave an additional spring to her steps.

"I'm on my way."

***

John Sheppard was bouncing impatiently on the balls of his feet, hands shoved deep in his pockets, when Sam arrived at the isolation room. He stood outside the door, his eyes fixed on the small window that was his only means of contact with Elizabeth right now. His jaw was set, his eyes, hard as diamonds, narrowed in concentration as he mulled over the events of the last few hours. Sam approached him carefully, allowing him to get accustomed to her presence before she talked to him. She had been in his place many times over the years - not in a situation like this, but she understood whirlwind of feelings that she imagined John would be experiencing: hope, worry, frustration, confusion at finding himself face to face with someone he had let go and mourned for.

"Colonel." He nodded at her as she stepped up to him, her eyes following the line of his gaze to where doctors and nurses wearing masks were swarming all over Elizabeth. She recognized Keller's small frame among the nurses and, in a corner, McKay, hunched over his tablet.

"Ma'am." Sheppard took a slight step to the side to make more room for her, but his eyes remained glued to the table where Elizabeth Weir, clad in a hospital gown, was being poked and prodded by the people she had once commanded. Eyes low, her expression demure, she collaborated patiently with the medical team.

"I just got word from Keller that they have her test results."

Sheppard licked his lips uncomfortably and nodded, but didn't say a word. "She hasn't said anything yet, they were waiting for you." He stepped forward and rapped on the window. Three heads snapped up, including Weir's. Sam saw her eyes search for the Colonel's, but he averted his gaze before they could meet. She could not blame his reticence, yet a sympathetic, and somewhat apologetic smile found its way to her lips as she caught the woman's eyes herself. Weir nodded in understanding, and Sam felt a small wave of relief releasing the tension in her shoulder. Elizabeth, whether human or cyborg, knew exactly the risks that a situation like this would entail for the Pegasus Galaxy - and potentially, Earth - if emotions got the better of the expedition leaders and allowed an enemy to infiltrate Atlantis. If their roles were reversed, Sam was sure Weir would have acted in the exact same way.

Her eyes darted to Keller for a moment as the doctor stepped outside the room and into the decontamination area. Next to her, John sighed quietly and widened his legs slightly, as if trying to find more solid footing to withstand the coming news like he would a strong gust of cold wind. John had never struck Sam as a very extrovert personality, but they had built a positive relationship over the months she had led the expedition, and his reaction to Elizabeth's alleged recovery was making her uncomfortable. Mixed feelings on the part of those who had worked in close contact with Elizabeth were to be expected, and she encouraged all the members of the flagship team to visit Dr. Heightmeyer to discuss their thoughts and feelings. She most definitely made sure Rodney had, before she allowed him to get into the same room with 'Elizabeth' (be in Elizabeth's presence). She debated whether it would be a good idea to order John to talk to the psychiatrist, regardless of the outcome. He seemed to take it harder than the others, except maybe Carson, who was still working through his own feelings about being a clone. The creaking of a door announced Dr. Keller's presence moments before she joined them in the observation room.

"Colonel Carter. Colonel Sheppard." She nodded at both of them.

"Dr. Keller. I hope you bring good news." The young doctor pressed her lips together.

"We ran every test we could," she started, pointing to the tablet in her hands. "even Dr. McKay ran out of ideas eventually." The ghost of a smile played on Sam's lips. He and his team of scientists had run all his suggestions for additional tests by her before putting them into action. She could not have done better herself. "The results say the same. There are no traces of nanites, dormant of otherwise, in 's body."  
Sam released the breath she hadn't realize she'd been holding as John did the same next to her. "How is that possible? McKay said she needed the reactivated nanites to survive after the accident." The objection was on his lips before Sam could voice it. Keller nodded, clearly expecting this issue to be raised. She tapped on the tablet with nimble fingers and handed it to Sam. The screen showed two scans of Elizabeth's body, one showing the concentration and location of the nanites, the second entirely blank. "It is consistent with the version Dr. Weir has provided us. If she had indeed ascended, she would now be reincarnated in a new flesh and blood body. One that has not gone through the accident." She produced a second paper. "Dr. Weir had this scar on her knee, from a horseriding fall when she was a child."

"I remember this." John said absent-mindedly, and took a closer look at the picture showing a close-up of the scar.

"This is from an old check up" Keller mentioned. "But the scar is no longer there, as if it had never existed."

"Daniel had something similar happen to him." Sam nodded, remembering an ongoing joke between Jack and Daniel about Jack wanting to ascend to fix his bad knee without worrying about insurance costs.

"So this is..." John trailed off, almost afraid to say the words.

"Dr. McKay's team is going through all possible intelligence channels to investigate whether the replicators have had any history of being capable of cloning actual human bodies, but yes, the woman I have examined is 100% human. She also has Elizabeth Weir's memories up to several months into her captivity on Asuras."

Out of the corner of her eye, Sam saw John flinch at the mention of the time Elizabeth had spent as a prisoner to Oberoth.  
"I have no reasons to doubt her story at this point," she continued, "but I would like to keep her under observation for a couple more days, to check whether we might have missed something. If she has been planted by the replicators as a Trojan horse, whatever Elizabeth is programmed to do may not emerge until later, when we have all regained her trust in her." Keller ran a hand through her mussed hair. "As I have said, I doubt the replicators have found a way to clone a flesh and blood version of Elizabeth, unless they have struck up an alliance with a civilization who possesses the technology."  
Sam nodded. "We will continue gathering intel."

"However," Keller continued, "her physical conditions appear to be compatible with a return from ascension rather than cloning." She conjured up her first assessment of Elizabeth, right after she had been found, in a local village near the Alpha site, over a week prior. "When we found her, she claimed that she had no recollection of who she was, or why she had ended up where the farmers found her, which is consistent with what we know of Dr. Jackson's experience. A clone would retain all their memories and be complete unaware of being a copy."

"What if she knows and she's just lying to us?" John objected again, his lips tight in a hard line. If Sam had a dollar for each time she had heard Sheppard voice that particular thought, she would be able to afford a new naqadah generator for the SGC.

Keller pressed her lips together, offering an awkward smile, and shared a knowing look with Sam. "That is clearer to us now. If we look at all the MRIs we've taken over the course of the past week, we can see a distinct change in brain activity around two days ago, when she started to remember." More windows started popping up on the screen, showing brain scans. "We don't have the same amount of data available for Dr. Jackson, but the two scans we were able to retrieve show a similar development, although on a much smaller scale." She paused for a moment, to let the information sink in. "We still can't be sure 100%, but I think we can afford to be optimistic. The story is sound."

Sam sighed in relief. "This is good to hear. I will inform the IOA and the SGC as soon as I have your official report. And, uhm, how is she, emotionally speaking?"

"She is doing fairly well, considering the situation. She's still a bit disoriented. And frustrated. She still has memory blanks, and on the other hand, she's losing the few memories she has of being ascended. Dr. Heightmeyer's psych evaluation was positive, all things considered. She will need time to readjust."

"We all do," Sam said, more to herself than to others. "Would you recommend I send over again?"  
"It could be a good idea, yes. It would also be good for her to see more familiar faces in person, rather than the same medical staff in hazmat suits." Her eyes shifted towards John."I think it would be beneficial for everyone if people started paying short visits. Just a few people for a few days -you, Colonel Carter, as well as you and your team, Colonel Sheppard. I'm sure she will appreciate seeing someone who is not McKay."

"I, uh, will tell the others." he said.

"Dr. Jackson will be arriving tomorrow via Stargate," added Sam "I think it will do her good to share her experience with someone who has gone through the same thing. And it will help dissipate any leftover doubts that we may have."  
"Yes," Keller agreed. "If everything goes smoothly, we'll be able to bring her back to Atlantis in a couple of days. With your and the IOA's permission, of course."

"Of course. Well, why don't I come in and tell Elizabeth about Dr. Jackson's arrival?" Sam asked. She hadn't talked to Elizabeth since she had regained her memories and she was curious to see whether she was anything like the woman she remembered.

"Yes, I'll get you some protective gear. I think it's no longer necessary, but you know protocols. Colonel Sheppard, would you like to come in as well?"

John shook his head. "I think I'll come back some other time. I have to go back to Atlantis for mission prep. If you may excuse me. Doctor, colonel. " He gave a small bow and walked out of the building.  
Sam followed his retreating figure until he was out of sight. A nice, long talk with Dr. Heightmeyer was in order.

***

The talk with the IOA could have been worse. Daniel's solid presence throughout the ordeal kept Elizabeth's nervousness in check and her tongue firmly in her mouth even when she was tempted to snap back at the bureaucrats. She had always had a soft spot for Daniel, his enthusiasm and his endless knowledge of the ancients, and that hint of dorkiness that still lurked behind a personality hardened by war and loss. His gentle words, the warm, large hand on her shoulder, the trust she read in his eyes gave her a renewed sense of hope. Reaching out, and finding understanding and acceptance stirred feelings in her that she hadn't known she had suppressed. It would be a long road for her, and everyone involved in Atlantis, but she felt that he had helped ease some of the fear that was shrouding her. She had spent so many months in the dark depths of space, holding on to those memories of them. Her flag team. John, Teyla, Ronon, and even Rodney. It was those memories that kept her sane, all those little reminders of friendship and trust that fueled the flicker of warmth that the nanites in her body and the pain she suffered at the hands of Oberth could never smother. And yet, now that they were there, at her fingers' reach once again, eager - most of them - to show her the same respect and appreciation, she was not sure that she could embrace it fully, or even bring herself to give it back.  
She felt grateful, though. Daniel was there every little step of the way, a safety net in the whirlwind of meetings and talks, or downright questionings, that she had to endure right after she was cleared. She could not have hoped for a best medical team. In those first few terrible days, where her fate had depended on her test results, Carson and Jennifer had tried their best to make her feel at ease. It took her some time to get used to seeing the good doctor again, after she had mourned for him what felt a lifetime ago.

Teyla brought her a steaming mug of Athosian tea, on her first day out of confinement.

"Thank you, Teyla." She smiled as she closed her hands around the metal mug, welcoming the heat spreading into her fingers.  
"You are welcome, Dr. Weir." Teyla nodded and then bowed her head towards her. Elizabeth did the same, albeit awkwardly, performing the traditional Athosian greeting.

"We are very glad to have you back." Teyla said as she stepped back.

"It's good to be back," Elizabeth sighed, "even though this is not Atlantis." She gestured to the room they were in, bare but for a twin bed, a table with a chair and a locker. They had let her out of the infirmary, but she hadn't been granted permission to rejoin the mission in Atlantis yet. While Drs. Carter, Keller and Heightmeyer had signed all the necessary papers to have her moved into guarder quarters in the city, the IOA was still evaluating the request. "Still better than the isolation room, of course." She specified as she took a long sip of hot tea. "And this is wonderful, Teyla." She took another sip, letting the amber liquid wash away all thoughts of the IOA, and concentrated on her human body's reactions to the beverage. She had forgotten what it felt like to be dependent on organic fuel, and how satisfying fulfilling her biological needs could be. "God, I missed this." She whispered into the mug. "I missed all of you." She said then, aloud, her eyes scanning the room to meet those of her friends.  
Indeed, Ronon and Rodney were there as well, a half step behind Teyla. Ronon sported a small smile on his usually unreadable face. "'s good to see you". He nodded and gave her shoulder a light affectionate squeeze. Her hand came up to touch his briefly, before he stepped back and let Rodney step in. She barely had the time to set her mug on the table before she was enveloped in a tight hug. McKay had been with her quite often in the infirmary, but as concentrated he had been on checking the results of her tests, and on coming up with new methods to verify that she was indeed the human Weir, their contact was kept to a minimum.  
"I couldn't wait to do this without that stupid hazmat suit." She muttered into her neck. They both had to wipe a tear or two from the corners of their eyes as they released from the hug. She gestured for them to sit on her bed, and she eased herself into the single chair at her table.

"When will you be back to Atlantis?" Teyla asked.

"Well, actually, I don't know yet. The IOA hasn't signed for my release yet. There is still a chance I will be confined here for a while. Or sent back to the SGC as a long term guest". Her eyebrows rose sarcastically at the word guest. It was obvious that, if she were to be sent back to the SGC, it would be unlikely that she would see the world outside of Cheyenne mountain ever again. The thought scared her. On the other hand, she had faith in both Colonel Carter and General O'Neill and their abilities negotiating with the IOA. Well, Colonel Carter's, at least. "Security clearance would be an issue, at least at the beginning," she said, more to herself than Teyla, "I don't know what they would make of me, even if I was ever allowed back to Atlantis". She sighed ruefully, her thoughts forcefully taking her to the sunlit gate room, her office, and the tower where her life had changed forever. Still, she missed the city with a strength she thought unimaginable. And not only the city itself. As grateful as she was for her friends' presence, there was someone she had expected to see who was not there with the rest of his team.

"They'll let you in eventually. You're too valuable to the expedition. The information you must have gathered during your time," he gestured vaguely, uncomfortably avoiding her gaze, "away...the IOA will want to negotiate. And everyone else is on your side."

She flinched at the mention of her time with the replicators, but giving it a second thought, she agreed with Rodney. She nodded. "That actually makes sense, Rodney. Thank you."

She smiled gratefully to Rodney, Ronon and Teyla even as her mind drifted back to John and his absence. Was he still on her side? She hadn't talked to him in person yet. She had seen him lingering outside the infirmary windows, staring with hard eyes and lips pressed together, and she was fairly sure he was on the Alpha Site right now, along with the rest of his team. But refusing to see her. She tried to concentrate on the people surrounding her, but the warmth of their presence could not steer her mind away from that thought. If anything, the intimacy of the situation made his absence more noticeable to her, and the feeling of displacement and discomfort grew again in her chest.  
Teyla eventually stood from the bed, the others following suit. "I'm afraid we have to go back to Atlantis now. We have an off-world mission scheduled for the afternoon."

"Of course. I wouldn't want to delay you. Thank you for your visit, and I hope to see you soon."

"We'll bring you chocolate." Rodney beamed.

"If you don't eat it all first." Ronon smirked, and Elizabeth found herself chuckling alongside her friends, feeling, if only for a moment as if nothing had ever happened, and she wasn't considered a potential threat by her own people.  
They hugged again, and when she bowed to touch foreheads with Teyla, she could not stop her lips from forming the words: "is John okay?"

Teyla sighed. "Colonel Sheppard is having difficulties adjusting. He was upset for a long time after your disappearance. I am sure he will come and visit you as soon as he is ready. I assure you he has missed you very much." She squeezed her arm affectionately before she stepped back. "We'll be back as soon as possible". She bowed again and with that, Elizabeth found herself alone again, with only her thoughts to keep her company.

She curled up on the bed and picked up one of the books Carson had brought for her, hoping to find a few minutes of blissful distraction in the familiar words of Jane Austen.

***

"Why didn't you come in? Don't you want to talk to her?" Rodney nagged again as they walked towards the gate. Head down, John picked up his pace, putting more distance between him and the scientist. "You should be as happy as we-"

"We've been through this, Rodney," John growled through his teeth, "I don't trust her yet."

"What more evidence do you want? We've been-" Teyla's hand on his arm interrupted the flow of his words. "Let it go, Rodney," she said softly, nodding towards the stiff frame of the colonel punching in the coordinates to Atlantis. "But-" the scientist protested.

"Leave him be." Teyla reiterated. "John will realize in due time that his behavior is affecting and all of us. Or so I hope." She sighed, her eyes following John as he stepped through the gate without as much as a glance back to his team.

"This is insane." McKay insisted, and with a resigned shake of his head, he followed his teammates through the event horizon.

***

He knew she would be coming back tomorrow. He had known for days now, and the thought still terrified him. His talks to Dr. Heightmeyer hadn't helped much either. If he didn't trust the doctor's abilities completely, he would suspect that she, too, was starting to resent him for his attitude towards the whole Elizabeth ordeal. It was understandable at the beginning, they had all been shaken, but as the news of her return from ascension sank in, everyone started to warm up to the idea of Elizabeth coming back to Atlantis. He had found a good confidant in Colonel Carter at the beginning, but as she opened up to Elizabeth he eventually found himself alone with his doubts and fears. Voicing his opposition to her reinstatement in the expedition didn't bear any results. If any, many felt that he was betraying his old leader, or had sold himself to the IOA for a promotion to commander of Atlantis. John laughed bitterly at their conjectures. Part of him even wished it was that easy.

Even his team avoided him now. Or it was the other way around. Yeah, more like it. He didn't want to hear them discuss their latest visit to Elizabeth, talk about what they were going to bring them or what would happen when she would be back.  
The only good thing that came out of this was that Rodney's incessant babbling had stopped. Their communication happened mostly via written messages or short sentences, and it was always work-related. Still, John was sure Rodney wasn't angry with him, just intimidated, or tired of being yelled at for all his effort. Teyla, however, was a completely different matter. He had tried to elude her queries and her offers for Athosian tea and conversation, but she was either perfectly aware of his issues, or she had a very strong inkling. Her questions were daring, teasing, challenging him to respond aggressively and prove her theory. Where Heightmeyer used poise and calm to coax an answer out of him, Teyla had quick wit and banto sticks. They had finished a particularly intense session when she brought up the issue again. After those minutes of blissful silence, with his mind and body focused entirely on their sparring match, the weight on his chest almost knocked his breath out of his lungs.

_"Elizabeth is coming back tomorrow." Teyla said, wiping beads of sweat from her forehead.  
"I know. I scheduled the trip myself."  
"Will you be there to welcome her?"  
John took a swig from his bottle. "I don't know."  
"You are the military commander of this place."  
"I might have other engagements."  
"She's your friend John."  
"She used to be. That person is gone."  
"That person is at the Alpha Site right now wondering why you don't want to talk to her!" Teyla swirled around. Her movements, brisk sharp, betrayed her anger. His nostrils flared, and it wasn't for want of oxygen.  
"Enough, Teyla."  
"She's hurting, you're hurting, and this whole situation is detrimental to your people. And me." Words flew freely from her lips now. "You can't avoid her forever."  
"I'm done with this." He bent to retrieve his bag and turned to leave.  
"You can't avoid yourself forever, either. John!" Her words echoed in his mind as he stormed away to the nearest transporter. _

John slipped into his uniform pants and sat on his bed with a sigh. He'd always loved to hear Teyla's thoughts on issues that bothered him, but this was different. Too much, and too close. He had seem his fair share of tragedy and ethical dilemmas in his life, even before he joined the Atlantis expedition, but the scope of what had happened in the past year, after Elizabeth's accident, was too much for him to wrap his head around. The surgeries, the nanites, losing her to the replicators only to find a clone of her around every damn corner of the galaxy. So similar, and yet so different from the Elizabeth he knew. Each time a little bit of hope of bringing her home was shattered, until one of the replicated Elizabeths informed them that their - his Elizabeth - had died at Oberoth's hands shortly after she was captured.  
He refused to believe her at the beginning - who would trust a replicator anyway - but as time went by and no other signs of Elizabeth, human or otherwise, were found, the expedition started reducing their searching efforts until the operation was abandoned altogether.

For a long time he had felt that Atlantis had failed Elizabeth. The SGC even more so, as they didn't waste any time in sending Colonel Carter to take over the role of expedition commander mere days after Elizabeth's disappearance. And yet, the only one he could never forgive, down deep in his heart, was himself.

He should have never left her on that ship. He should have pushed harder to put a rescue mission together as soon as he'd come back from that operation without her. They should have kept the clones captive until they could acquire some actual information from them. Could've, should've, would've...John let his body fall back onto the mattress and scrubbed his face with his hands. He couldn't wrap his head around Elizabeth as an ascended being. He had met his fair share of ascended people meddling with mundane affairs, and he couldn't imagine Elizabeth as part of that crowd. Most of all, he could not accept the thought of Elizabeth actually dying and coming back. He knew part of the mechanics behind ascension, but the idea that ascension could only occur when the body was on the very brink of death made his stomach fall. Thinking of Elizabeth's last moments before ascension made his stomach gurgle threateningly.

_What happened to you? Who are you now? Are you the same person I left on that ship?_ Those questions had been haunting him since her return. Questions he both craved and dreaded to ask.  
_Do you hate me for leaving you there?_

He took a shaky breath and rolled onto his side, his arm reaching out to grab the round vase on his nightstand. It was the clay vase he had given her for her birthday on their first year on Atlantis. He'd refused to ship it back to Earth with the rest of her things, and it had been sitting in his room ever since. Even though only four years had passed, to him it felt like a lifetime ago. Cut off from Earth, still on Lantea, each of them trying to find their own footing in the situation and with each other, scared, excited and oblivious of what was yet to come...a bittersweet smile found his way on his lips as he opened the vase. He fished out an Athosian necklace he had bought for her during her second birthday on Atlantis, and a birthday card that had accompanied the following year's gift: a basket of Earth junk food that had lasted maybe two days.  
There were two pictures inside the vase as well: a group picture of their first days in Atlantis, complete with General O'Neill's magnum bottle of champagne, and a picture of Elizabeth he had taken on the balcony off her office. He didn't remember why or how he took that photo, it was probably meant as a joke. He was certain of one thing though: he did not know, at that time, that this would have been the last picture of her before they lost her to the replicators, mere days later.

He ran his thumb over the glossy surface of the photo, first over the dark, long curls of her hair, then over her shy smile. Her head ducked, she still looked at the photographer, her eyes half-reproachful, half-embarrassed, and yet unequivocally amused.

_What happened to you?_ In his mind, the image morphed into a memory of Elizabeth on the operating table, her head shaved and the corner her mouth stretched by the respirator. And then kneeling, screaming as Oberoth forced his thoughts into her mind.  
His stomach churned again and he felt his lunch bubble up his throat.

"Oh, God." John dropped the picture on the bed and lurched towards the bathroom.

***

He was leaning on the balcony overlooking the gate room when she came back, escorted by his team and two guards. It was the first time their positions were reversed, he thought. He was usually the one coming back via gate, his eyes immediately going up to find her eyes, to reassure her that he was safe, and so was the city.

"Welcome back Dr. Weir." He heard Carter say. Elizabeth looked small and overwhelmed in the room that she had once filled with the mere strength of her presence.  
The crew took that as the cue to erupt in an ear-splitting applause. Cheers came from the consoles behind him, especially from those who had been with the expedition since the beginning. He looked back to see Chuck and Zelenka patting each other on the back, and he wished he could share in their enthusiasm.  
As he turned his gaze down to the gate room, he found his eyes locked onto hers. He could read the questions and the hurt in them for a split second before she shifted her attention back to Carter, who was handing her an earpiece.  
She stepped forward on to the center of the gateroom as she adjusted the microphone. She looked around herself, drinking in her surroundings, the city and the people that she loved so much, and her lips finally lifted in a smile.  
She tapped her earpiece, and her voice filled every room in Atlantis for the first time in a year.

_"Atlantis, this is . First of all, I want to thank you for your incredible welcome. I've missed you all terribly."_  
Her voice broke, and another round of applause swept through the control room. Her voice boomed in John's head, and his heart pounded violently against his ribcage.  
_"Some of you who have arrived to Atlantis only in recent times may have never met me in person, but I am sure that by now you must know who I am, and what circumstances caused my absence from Atlantis." She took a deep breath. "I don't know what role, if any, I will have in this expedition in the future. As of now, I am just incredibly grateful to stand here, in this city that I consider my home, surrounded by wonderful people that are like family to me. For a long time I thought I would never see you again, and yet adversity has not prevailed. I am sure that you have done some amazing things here in the past year, and I cannot wait to talk to all of you in person once I am settled in. I hope, with all my heart, that I will be able to join you soon, in any capacity that I may be allowed, and work side by side with you once again. It is overwhelming to be here."_ Her hand went to her eye to wipe a tear, and John had to close his eyes as a wave of raw emotion washed through him.

"I'll let you go back to your stations now. I will see you soon. Thank you." One last applause marked the end of her speech. As the crowd dispersed and people went back to their work, chattering excitedly, John stayed in place, watching Carter and the others hug Elizabeth before his team and the guards escorted her to her quarters. Her old quarters. He had seen to it personally that she would be assigned to her old room, and that her things would be sent there before her arrival. She would have to take a trip to Earth soon, to see her mother, but that could wait a little longer.

After his team left with Elizabeth, he joined Colonel Carter in the gate room.

"That was nice, wasn't it?" She said, offering him a tentative smile.

"Yeah," He agreed. "Everyone looked satisfied."

"John," she started, "I was going to ask Carson to bring Elizabeth some lunch in an hour or so, once she's settled, but I thought I could give that task to someone else." She looked at him expectantly. "What I mean is-"

"Fine," he, said, his tone flat even as his heart rebelled to the thought. "I'll do it."

***

Elizabeth stacked her folded shirts neatly into one of her drawers and stood up with a sigh of relief. The few boxes she had found upon her arrival in her quarters were now empty, and the room had regained a certain degree of familiarity. She read her mother's note over and over, and part of her wished she could go back to Earth to hug her and tell her everything that had happened in the past year - or four. She clutched her father's clock in her hand, glad that the keepsake had somehow found its way back to her. She set it on her desk, next to a picture of her mom with Sedge. Teyla had come by with a fresh mug of Athosian tea and a small pile of books that had originally belonged to her library. She arranged them on the shelf alongside the other ones that had come from Earth. With a small plant or two and a couple of paintings as a finishing touch, the room would feel like she had never left it.  
She sat at her desk and turned on the tablet they had given her. It was not yet connected to the Atlantis network for security reasons - just in case she *was* a robot, after all - and it only included limited content, but at least she could read up on what had occurred in Atlantis and the Pegasus Galaxy in the past year. Or at least, what they wanted her to know. And Rodney had set it up with solitary, which amused her and made her tear up at the same time.  
The screen lit up and showed a number of folders named by month. She tapped on the one dating back to her disappearance, and a list of files appeared, categorized by topic. She filtered out the files including the keyword 'asura', opened the oldest one and started reading.  
She was merely ten lines in when her doorbell chimed.

"Yes?" She asked, getting up from her chair. She wasn't expecting anyone, and only a small number of expedition members were allowed to contact her independently.  
The door wooshed open, and her breath caught in her throat when she saw John standing in the doorway, a mess hall tray balanced on one hand.

"Hey," he said awkwardly, the tip of his tongue coming out to wet his lips. "I'm here too, uh..." He nodded down at the tray.

She opened her mouth but no sound would come out. She cleared her throat. "Sure. Sure, come in. Put it on the desk."  
He did as he was told and then stood there, looking at her but avoiding eye-contact. It felt strange, standing in front of him after so long. He was exactly how she remembered him, and yet he felt like a complete stranger. She realized for a moment that he was probably thinking the same of her, but she wasn't in the mood to get into his mind. She had done it quite extensively during the past few weeks, wondering why he refused to see or talk to her, and conjuring up an endless list of plausible reasons that could have kept him from coming to the Alpha Site with the rest of his team. Rage and frustration built within her, and she had no intention of bottling them up. Not after she had spent months hiding them in the darkest recesses of her mind: her feelings and most precious memories, so that Oberoth may not access them. So that he could not use them to hurt her, Atlantis, and him.

"Why are you here, John?" She asked, her voice low, questioning, probably frostier than she had intended. John indeed winced.

"I'm sorry, I know I've been a massive asshole." He blurted out. "I should have come to see you with the others. I should have been more supportive. I was all caught up in my pain and fears and did not stop to think how you must have been feeling."

She shook her head. "What pain and fears, John? I was the one to be transformed into a- a goddamn cyborg and then left behind on that ship. I was the one to be violated and tortured, sometimes for information, sometime just for the sake of it. I was brought to brink of death over and over, until I ascended. I wish that I could tell you how that was, because I don't even remember that time of my existence, John. It's just a vague recollection of white figures of light. And then I was unceremoniously dumped on the Alpha Site only to spend weeks surrounded by people in hazmat suit, poking and prodding me to make sure I'm not a copy hell-bent on destroying Atlantis." The words flowed out of her mouth unconstrained, her voice raising with each sentence, as unwanted memories flooded her mind and threatened to overwhelm them once again. "I had people supporting me then: Rodney,Teyla, Ronon and Carson. Even Carter and Daniel. And yet I had expected to find you at my side, as always. I thought that even though I don't even know who the hell I am anymore, I could count on you ease some of the burden. I never had to put my faith in you into question, until now." She took a shaky breath. "I needed you with me John."

When he spoke again, he looked like kicked puppy, head low and tail between his legs. "I was scared, Elizabeth. That you could be another clone, robot, sleeper agent, hallucination, or whatever else this galaxy may have to throw at us, and I would have to go through the process of losing you once again. I don't know whether I could have done it."

He looked at her as she seemed to ponder his words. She looked exactly as he remembered her, down to the spray of freckles on her nose and the little rebel curl that she kept tucking behind her ear. She was wearing one of her old uniforms, grey pants and a red shirt. The wave of nostalgia that crashed through him threatened to knock him off his feet. He closed his eyes, steadying himself against the tide of emotions that he had so expertly learned to stifle in the past year.  
"I was scared to let myself open up to you and have you taken away from me again. It was so hard to say goodbye the first time that- this sounds incredibly stupid, doesn't it?" He reached out for her only to have Elizabeth flinch away from his touch.

"It's not stupid, John." She conceded. "It's human, protecting ourselves from pain." She moved to her bed and sat down on the mattress. "But God, John, I needed you. I needed you on that ship, to come and take me away from that living hell. And I needed you to be there when I was quarantined on the Alpha site. Hell, John, I would have wanted you to step with me through the gate when I arrived earlier."

"There was nothing more I wanted than to bring you home and blast Oberoth into a million tiny pieces, Elizabeth, if I'd had the power-"

"I know. And I don't want to hold this against you." Except that she still did, to a certain extent, and it would take a long time and many other chats before she could look at him and the others without the ghost of resentment polluting her feelings for them. She scuffed the floor with the heel of her boots, thinking.

"Were you the same, when Carson came back?" She asked, looking up at him.

He shook his head. "You're not Carson, 'Lizbeth. It's different with you. It was _always_ different with you." His voice lowered to a whisper and he took a tentative step forward. He held out his hand again, and this time she took it, her fingers wrapping gently around his.

"I can't change what happened, or my behavior in the past month. I just- I just I want you to know that I'm here to support you." His thumb rubbed gentle circles on her palm. It was an exercise in restraint, not to bury his face in her hair and let the tears flow freely. "I'm sorry."

She yanked her hand away from his and stood up again, suddenly angry. "What if you get scared again, John? What if it becomes too much for you to handle?"

"I don't want to let you down, 'Lizbeth."

"But you did!" She clenched her fists at her side, trying to control her temper when all she wanted was to scream at him and hit him with all the force she could muster. _I needed you. I needed you and you weren't there._

"I know, dammit." He growled. "There isn't a day in this galaxy that I don't relive that mission and think that I should have been able to do something more because I had sworn to protect you. And I wasn't able to.

He took a deep breath. "Back in McMurdo, you were the first to trust me, remember? You gave me a second chance at making something good out of my life. You made a gamble that day, you put your trust in me and I failed you."

She thought back to those days on the Antarctica base, fighting with the IOA so she could have him on her team. He had given her plenty of reasons to want to kick his ass all the way back to Earth during those first few months, and yet they'd managed to find their balance. She couldn't have wished for a better partner in taking care of Atlantis.

"And- what are you asking me, John? To take another gamble? I don't have the strength to steer you, to keep you focused. I don't even know who I am anymore."

"Let me show you then. Let me show you how I see you. How the others here see you."

She sighed. "I can't make any promises, John."

"I'm not asking for promises. Just that you won't cut me off." He said. "...like I did to you." He added, his voice broken. "Are we beyond repair?"

She sighed. "This will not be easy, John. Getting used to life in Atlantis again, working through what happened in the past year, re-building my relationship with you and everyone else...only time will tell." Her eyes shifted towards the table where the tray had been sitting abandoned. "Now excuse me, but I'm a bit hungry. And tired."

"Yes. Enjoy your lunch and if you need something - anything - else, call me, okay?" He said as the doors to her quarters slid open to let him out. "I hope I'll see you soon."

She nodded, offering him a small smile that kindled a flicker of hope in his heart. "See you soon."

***  
**Epilogue - six months later**

"John, this is Carter. You and your team are expected in the gate room in 15 minutes." Carter's voice crackled in John's ear as he was sliding his gun in his thigh holster.

"Copy that. Team's assembled and almost ready to leave."

"Very well, I'll see you in a bit. Carter out."

"Rodney, do you have the samples from botanics? I don't want to show up on that planet empty handed." He asked.

"Of course I do. Right here." The scientist patted the black bag in satisfaction. "Got them straight from Katie's very delicate hands."

"Speaking of hands, I believe it was your intention to propose to Dr. Brown soon." Teyla said, earning a blush from Rodney.

"Don't you have that saying on Earth?" Ronon quipped in. "If you like it then you should put a ring on it."

The blush deepened. "That is not even an Earth saying, it's a stupid pop song." He stuttered. "Besides, the lyrics are different."

Ronon flashed a smirk at Elizabeth, who was tying up her combats. The corner of her lips lifted only slightly, but her eyes betrayed her amusement at the banter. Ever the diplomat, she laid a gentle hand on Rodney's arm.

"Rodney, we're just eager to see you happy with the person you love."

"I see your diplomatic skills are still as sharp as I remember them." Teyla whispered to Elizabeth as they retrieved their own firearms from the rack, and Elizabeth had to stifle a chuckle. This was not her first off-world mission with the them, but her appointment as official member of the flagship team of Atlantis was still new enough that every briefing, every preparation, every step on a foreign planet was accompanied by a flicker of enthusiasm that she had once suspected could not be rekindled.

Carter had been right. With her knowledge of both the Ancients and the Asurans, she was too valuable to the expedition. Once they had finally made peace with the fact that she was not to turn on them and transform into a deadly Terminator, and Heightmeyer was satisfied with her psychological conditions, the IOA finally caved and allowed the Colonel to reinstate Elizabeth as a full-fledged member of the expedition and assign her to a working team.

"Let's go, I want to stop by the mess hall and get some extra snacks." Rodney started towards the transporter.

Ronon's face became suddenly interested. "That's the best idea I've heard from you all day." He set off after him, Teyla on his heels.

Thinking back to her scarce lunch and the lone power bar in her backpack, Elizabeth made to follow them, but a force kept her from moving. Namely, John's hand pulling on her backpack.

"Where do you think you're going, doctor?"

He spun her around gently and hooked a finger into the hem of her combats, tugging her close, a smirk ghosting over his lips. She rolled her eyes in mock exasperation, but she indulged him, leaning in for a soft kiss. One of her hands found his and squeezed gently, their fingers intertwining momentarily.  
He ran his nose up the side of hers tenderly, giving her a last peck on the lips before he released her.

"Come on, let's get these negotiations going."

John made another playful grab at her and waltzed out of his reach, rushing after her new teammates.


End file.
